Lt. Gen. Cirilito Sobejana said an unspecified number of militants, including gunmen belonging to the Bangsamoro Islamic Freedom Fighters, were wounded in clashes in the towns of Ampatuan and Datu Hoffer Ampatuan in Maguindanao province.
The bodies of five of the slain militants were recovered by government forces, he said, adding that 10 soldiers were wounded in the fighting.
The Islamic State group claimed that militants killed 43 soldiers using explosives while repulsing the recent military assaults in two Maguindanao villages, but Sobejana said the claim was "untrue."
Government forces launched air strikes and artillery fire on an encampment of the militants in Salman village in Ampatuan on Monday after receiving intelligence that the gunmen were plotting attacks, the military said.
Troops later assaulted the encampment and another group of armed militants in Datu Hoffer Ampatuan, seizing firearms, ammunition and homemade bombs, the military said.
The largest Muslim rebel group in the southern region, the Moro Islamic Liberation Front, signed an autonomy deal with the government in 2014, ending decades of separatist insurrection.
Its leader and many of its commanders have been appointed to govern a five-province autonomous region under a transitional setup, but smaller hard-line armed groups, including some that have been linked to the Islamic State group, have continued to fight the government.